Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primates in biomedical research. This species is critically important in efforts to understand the causes and potential new treatments for many human diseases. Rhesus macaques are a premier model organism for the study of the pathogenesis of HIV-AIDS, and for development of novel treatments and new vaccines against HIV infection. In addition, rhesus macaques are commonly used in studies of basic neurobiology, risk factors for psychiatric illnesses such as anxiety disorders and depression, metabolic diseases such as diabetes and osteoporosis, and reproductive biology. This project will dramatically increase the value and impact of this laboratory primate species for all types of biomedical research by generating a substantial amount of new information about genetic variation within the species. It is well established that genetic differences among people influence their risk of developing many, probably most, diseases including those listed above. Genetic variation can also influence the progression of disease and the responses of different people to a specific treatment. We will facilitate research concerning the genetic basis of disease susceptibility and response to treatment by identifying large numbers of new DNA sequence variants in functional genes and intervening sequences within the rhesus genome. To accomplish this, we will produce high-quality whole genome DNA sequence data for 433 rhesus macaques. The sequence data will be used to identify currently unknown DNA sequence variation present in this species, including single nucleotide variants, small indels, CNVs and other variants. The study subjects will be animals already characterized for one or more disease-related phenotypes, such as vaccine protection against SIV-AIDS, neurobiological traits, behavioral traits, metabolic disorders such as diabetes or polycystic ovary syndrome, and gastrointestinal diseases. By sequencing these animals, we will generate BOTH general information about variation across the macaque genome and specific information beneficial to the investigators who have phenotypically characterized these animals and contributed these DNA samples. All the data generated will be made publicly available through appropriate NIH and NPRC databases.